Hi,
From your email it's not clear if you're asking about loading
just one extra plugin, or an entire collection? If you're just
loading one or a handful, it is quite easy, and you can do something
very simple like this in your .vmdrc:

On Mon, Feb 03, 2014 at 02:04:55PM -0800, Daniel Russel wrote:
> Is loading molefile plugins from some place other than the VMD plugins
> directory something that is currently supported? If so, what is the best
> procedure? A couple of us have tried various permutations on `set
> auto_path` and `vmd_plugin_scandirectory`-based approaches without any
> success so far (with a plugin that loads fine if dropped in the vmd
> plugins dir of an install). If those are supported, do things like the
> directory structure under the provided path matter? That is, does there
> need to be an analogue to the vmd plugins directory or can I just point
> the directory containing the .so.
> On linux. VMD 1.9.1.A
> Thanks.